A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group.
A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group.
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DOI：
10.1186/1471-2148-7-9
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发表时间：
2007-01-29
影响因子：
3.4
通讯作者：
Imanishi T
中科院分区：
文献类型：
--
作者：
Kawahara Y;Imanishi T
在显着的表型进化期间，经常观察到谱系之间蛋白质进化速率的变化。我们还知道，在基因复制和丢失之后，参与这些事件的基因的蛋白质进化速率发生了变化，这是因为作用于基因的功能约束发生了变化。然而，在近缘物种的进化中，排除上述情况，蛋白质进化速率的变化频率在全基因组水平上仍不清楚。在这里，我们研究了蛋白质进化速率的恒定性在进化的四个密切相关的物种的严格意义上的酵母菌群（S。cerevisiae，S. paradoxus，S. mikeland和S. bayanus）。对于4个物种中明确定义的2，610个直向同源基因，我们在恒定速率和可变速率模型之间进行了似然比检验，发现344个（13.2%）基因在至少一个谱系中显示出蛋白质进化速率的显着变化。在所有经历速率变化的基因中，分别有139个和49个基因表现出加速和减速的进化。大多数的进化速率的变化可以归因于非同义位点上的选择性约束的变化，独立于物种特异性基因的复制和丢失。我们估计，在酵母属物种的进化过程中，蛋白质进化速率的变化以每百万年每个基因2.0 × 10-3的概率出现。此外，我们发现，经历速率加速的基因比经历速率减速的基因具有更低的表达水平和更弱的密码子使用偏好。蛋白质进化速率的变化可能经常发生在密切相关的酵母属物种的进化中。选择翻译的准确性和效率可能会显着影响蛋白质进化速率的变异性。
Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene duplication and loss, the protein evolutionary rates of genes involved in such events changed because of changes in functional constraints acting on the genes. However, in the evolution of closely related species, excluding the aforementioned situations, the frequency of changes in protein evolutionary rates is still not clear at the genome-wide level. Here we examine the constancy of protein evolutionary rates in the evolution of four closely related species of the Saccharomyces sensu stricto group (S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus). For 2,610 unambiguously defined orthologous genes among the four species, we carried out likelihood ratio tests between constant-rate and variable-rate models and found 344 (13.2%) genes showing significant changes in the protein evolutionary rates in at least one lineage. Of all those genes which experienced rate changes, 139 and 49 genes showed accelerated and decelerated evolution, respectively. Most of the evolutionary rate changes could be attributed to changes in selective constraints acting on nonsynonymous sites, independently of species-specific gene duplication and loss. We estimated that the changes in protein evolutionary rates have appeared with a probability of 2.0 × 10-3 per gene per million years in the evolution of the Saccharomyces species. Furthermore, we found that the genes which experienced rate acceleration have lower expression levels and weaker codon usage bias than those which experienced rate deceleration. Changes in protein evolutionary rates possibly occur frequently in the evolution of closely related Saccharomyces species. Selection for translational accuracy and efficiency may dominantly affect the variability of protein evolutionary rates.
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影响因子：
64.8
作者：
Kellis, M;Patterson, N;Lander, ES
通讯作者：
Lander, ES
影响因子：
10.7
作者：
Drummond, DA;Raval, A;Wilke, CO
通讯作者：
Wilke, CO
影响因子：
10.7
作者：
SAITOU, N;NEI, M
通讯作者：
NEI, M
DOI：
10.1073/pnas.50.4.672
发表时间：
1963-01-01
影响因子：
11.1
作者：
MARGOLIASH, E
通讯作者：
MARGOLIASH, E
DOI：
10.1073/pnas.85.8.2444
发表时间：
1988-04-01
影响因子：
11.1
作者：
PEARSON, WR;LIPMAN, DJ
通讯作者：
LIPMAN, DJ